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R-factors: Difference between revisions
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→what kinds of problems exist with these indicators?
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* (R<sub>sym</sub> / R<sub>merge</sub> ) should not be used to judge [[data quality]], R<sub>meas</sub> should be used instead. The reason is that the former depend on multiplicity, whereas the latter doesn't. | * (R<sub>sym</sub> / R<sub>merge</sub> ) should not be used to judge [[data quality]], R<sub>meas</sub> should be used instead. The reason is that the former depend on multiplicity, whereas the latter doesn't. | ||
* R/R<sub>free</sub> and NCS: reflections in work and test set are not independent if chosen randomly. It is better to choose the test set reflections in thin resolution shells (FIXME: references and programs for this). A paper investigating this thoroughly is Fabiola, F., A. Korostelev, et al. (2006). "Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry." Acta Cryst. D 62: 227-38. | * R/R<sub>free</sub> and NCS: reflections in work and test set are not independent if chosen randomly. It is better to choose the test set reflections in thin resolution shells. Since the twin related reflections have the same sin(theta)/lambda values they will not be split over the working and reference sets. DATAMAN (Uppsala Software Factory) [[XPREP]] (a program which may be obtained from Bruker) offers this option. A disadvantage is the the maps may not be quite as good as when the free R reflections are selected randomaly. (FIXME: references and programs for this). A paper investigating this thoroughly is Fabiola, F., A. Korostelev, et al. (2006). "Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry." Acta Cryst. D 62: 227-38. | ||
* Sets of reflections used for calculating R<sub>free</sub> should be maintained throughout a project. This is nicely discussed at http://www.bmsc.washington.edu/people/merritt/xplor/rfree_example.html . | * Sets of reflections used for calculating R<sub>free</sub> should be maintained throughout a project. This is nicely discussed at http://www.bmsc.washington.edu/people/merritt/xplor/rfree_example.html . | ||